Biomedical ontologies are emerging as critical tools in genomic and proteomic research where complex data in disparate resources need to be integrated. A number of ontologies exist that describe the properties that can be attributed to proteins; for example, protein functions are described by Gene Ontology, while human diseases are described by Disease Ontology. There is, however, a gap in the current set of ontologies—one that describes the protein entities themselves and their relationships. We have designed a PRotein Ontology (PRO) (...) to facilitate protein annotation and to guide new experiments. The components of PRO extend from the classification of proteins on the basis of evolutionary relationships to the representation of the multiple protein forms of a gene (products generated by genetic variation, alternative splicing, proteolytic cleavage, and other post-translational modification). PRO will allow the specification of relationships between PRO, GO and other OBO Foundry ontologies. Here we describe the initial development of PRO, illustrated using human proteins from the TGF-beta signaling pathway. (shrink)

The Protein Ontology (PRO) provides a formal, logically-based classification of specific protein classes including structured representations of protein isoforms, variants and modified forms. Initially focused on proteins found in human, mouse and Escherichia coli, PRO now includes representations of protein complexes. The PRO Consortium works in concert with the developers of other biomedical ontologies and protein knowledge bases to provide the ability to formally organize and integrate representations of precise protein forms so as to enhance accessibility to results of protein (...) research. PRO (http://pir.georgetown.edu/pro) is part of the Open Biomedical Ontologies (OBO) Foundry. (shrink)

The Protein Ontology (PRO; http://proconsortium.org) formally defines protein entities and explicitly represents their major forms and interrelations. Protein entities represented in PRO corresponding to single amino acid chains are categorized by level of specificity into family, gene, sequence and modification metaclasses, and there is a separate metaclass for protein complexes. All metaclasses also have organism-specific derivatives. PRO complements established sequence databases such as UniProtKB, and interoperates with other biomedical and biological ontologies such as the Gene Ontology (GO). PRO relates to (...) UniProtKB in that PRO’s organism-specific classes of proteins encoded by a specific gene correspond to entities documented in UniProtKB entries. PRO relates to the GO in that PRO’s representations of organism-specific protein complexes are subclasses of the organism-agnostic protein complex terms in the GO Cellular Component Ontology. The past few years have seen growth and changes to the PRO, as well as new points of access to the data and new applications of PRO in immunology and proteomics. Here we describe some of these developments. (shrink)

The Protein Ontology (PRO) web resource provides an integrative framework for protein-centric exploration and enables specific and precise annotation of proteins and protein complexes based on PRO. Functionalities include: browsing, searching and retrieving, terms, displaying selected terms in OBO or OWL format, and supporting URIs. In addition, the PRO website offers multiple ways for the user to request, submit, or modify terms and/or annotation. We will demonstrate the use of these tools for protein research and annotation.

Research has indicated that microRNAs (miRNAs), a special class of non-coding RNAs (ncRNAs), can perform important roles in different biological and pathological processes. miRNAs’ functions are realized by regulating their respective target genes (targets). It is thus critical to identify and analyze miRNA-target interactions for a better understanding and delineation of miRNAs’ functions. However, conventional knowledge discovery and acquisition methods have many limitations. Fortunately, semantic technologies that are based on domain ontologies can render great assistance in this regard. In our (...) previous investigations, we developed a miRNA domain-specific application ontology, Ontology for MIcroRNA Target (OMIT), to provide the community with common data elements and data exchange standards in the miRNA research. This paper describes (1) our continuing efforts in the OMIT ontology development and (2) the application of the OMIT to enable a semantic approach for knowledge capture of miRNA-target interactions. (shrink)

Identification of non-coding RNAs (ncRNAs) has been significantly enhanced due to the rapid advancement in sequencing technologies. On the other hand, semantic annotation of ncRNA data lag behind their identification, and there is a great need to effectively integrate discovery from relevant communities. To this end, the Non-Coding RNA Ontology (NCRO) is being developed to provide a precisely defined ncRNA controlled vocabulary, which can fill a specific and highly needed niche in unification of ncRNA biology.

In recent years, sequencing technologies have enabled the identification of a wide range of non-coding RNAs (ncRNAs). Unfortunately, annotation and integration of ncRNA data has lagged behind their identification. Given the large quantity of information being obtained in this area, there emerges an urgent need to integrate what is being discovered by a broad range of relevant communities. To this end, the Non-Coding RNA Ontology (NCRO) is being developed to provide a systematically structured and precisely defined controlled vocabulary for the (...) domain of ncRNAs, thereby facilitating the discovery, curation, analysis, exchange, and reasoning of data about structures of ncRNAs, their molecular and cellular functions, and their impacts upon phenotypes. The goal of NCRO is to serve as a common resource for annotations of diverse research in a way that will significantly enhance integrative and comparative analysis of the myriad resources currently housed in disparate sources. It is our belief that the NCRO ontology can perform an important role in the comprehensive unification of ncRNA biology and, indeed, fill a critical gap in both the Open Biological and Biomedical Ontologies (OBO) Library and the National Center for Biomedical Ontology (NCBO) BioPortal. Our initial focus is on the ontological representation of small regulatory ncRNAs, which we see as the first step in providing a resource for the annotation of data about all forms of ncRNAs. (shrink)

Biological ontologies are used to organize, curate, and interpret the vast quantities of data arising from biological experiments. While this works well when using a single ontology, integrating multiple ontologies can be problematic, as they are developed independently, which can lead to incompatibilities. The Open Biological and Biomedical Ontologies Foundry was created to address this by facilitating the development, harmonization, application, and sharing of ontologies, guided by a set of overarching principles. One challenge in reaching these goals was that the (...) OBO principles were not originally encoded in a precise fashion, and interpretation was subjective. Here we show how we have addressed this by formally encoding the OBO principles as operational rules and implementing a suite of automated validation checks and a dashboard for objectively evaluating each ontology’s compliance with each principle. This entailed a substantial effort to curate metadata across all ontologies and to coordinate with individual stakeholders. We have applied these checks across the full OBO suite of ontologies, revealing areas where individual ontologies require changes to conform to our principles. Our work demonstrates how a sizable federated community can be organized and evaluated on objective criteria that help improve overall quality and interoperability, which is vital for the sustenance of the OBO project and towards the overall goals of making data FAIR. Competing Interest StatementThe authors have declared no competing interest. (shrink)

In recent years, sequencing technologies have enabled the identification of a wide range of non-coding RNAs (ncRNAs). Unfortunately, annotation and integration of ncRNA data has lagged behind their identification. Given the large quantity of information being obtained in this area, there emerges an urgent need to integrate what is being discovered by a broad range of relevant communities. To this end, the Non-Coding RNA Ontology (NCRO) is being developed to provide a systematically structured and precisely defined controlled vocabulary for the (...) domain of ncRNAs, thereby facilitating the discovery, curation, analysis, exchange, and reasoning of data about structures of ncRNAs, their molecular and cellular functions, and their impacts upon phenotypes. The goal of NCRO is to serve as a common resource for annotations of diverse research in a way that will significantly enhance integrative and comparative analysis of the myriad resources currently housed in disparate sources. It is our belief that the NCRO ontology can perform an important role in the comprehensive unification of ncRNA biology and, indeed, fill a critical gap in both the Open Biological and Biomedical Ontologies (OBO) Library and the National Center for Biomedical Ontology (NCBO) BioPortal. Our initial focus is on the ontological representation of small regulatory ncRNAs, which we see as the first step in providing a resource for the annotation of data about all forms of ncRNAs. The NCRO ontology is free and open to all users. (shrink)

Representing species-specific proteins and protein complexes in ontologies that are both human and machine-readable facilitates the retrieval, analysis, and interpretation of genome-scale data sets. Although existing protin-centric informatics resources provide the biomedical research community with well-curated compendia of protein sequence and structure, these resources lack formal ontological representations of the relationships among the proteins themselves. The Protein Ontology (PRO) Consortium is filling this informatics resource gap by developing ontological representations and relationships among proteins and their variants and modified forms. Because (...) proteins are often functional only as members of stable protein complexes, the PRO Consortium, in collaboration with existing protein and pathway databases, has launched a new initiative to implement logical and consistent representation of protein complexes. We describe here how the PRO Consortium is meeting the challenge of representing species-specific protein complexes, how protein complex representation in PRO supports annotation of protein complexes and comparative biology, and how PRO is being integrated into existing community bioinformatics resources. The PRO resource is accessible at http://pir.georgetown.edu/pro/. (shrink)

Identification of non-coding RNAs (ncRNAs) has been significantly improved over the past decade. On the other hand, semantic annotation of ncRNA data is facing critical challenges due to the lack of a comprehensive ontology to serve as common data elements and data exchange standards in the field. We developed the Non-Coding RNA Ontology (NCRO) to handle this situation. By providing a formally defined ncRNA controlled vocabulary, the NCRO aims to fill a specific and highly needed niche in semantic annotation of (...) large amounts of ncRNA biological and clinical data. (shrink)

The Protein Ontology (PRO) is designed as a formal and principled Open Biomedical Ontologies (OBO) Foundry ontology for proteins. The components of PRO extend from a classification of proteins on the basis of evolutionary relationships at the homeomorphic level to the representation of the multiple protein forms of a gene, including those resulting from alternative splicing, cleavage and/or posttranslational modifications. Focusing specifically on the TGF-beta signaling proteins, we describe the building, curation, usage and dissemination of PRO. PRO provides a framework (...) for the formal representation of protein classes and protein forms in the OBO Foundry. It is designed to enable data retrieval and integration and machine reasoning at the molecular level of proteins, thereby facilitating cross-species comparisons, pathway analysis, disease modeling and the generation of new hypotheses. (shrink)

The Protein Ontology (PRO) provides terms for and supports annotation of species-specific protein complexes in an ontology framework that relates them both to their components and to species-independent families of complexes. Comprehensive curation of experimentally known forms and annotations thereof is expected to expose discrepancies, differences, and gaps in our knowledge. We have annotated the early events of innate immune signaling mediated by Toll-Like Receptor 3 and 4 complexes in human, mouse, and chicken. The resulting ontology and annotation data set (...) has allowed us to identify species-specific gaps in experimental data and possible functional differences between species, and to employ inferred structural and functional relationships to suggest plausible resolutions of these discrepancies and gaps. (shrink)

Critiquing any practice, theory, or law, requires understanding the characteristics of the environment which created a need for this law. There are hundreds of different cultures in the world, and each one has its own set of norms, characteristics, and values. What in one country is perceived normal, ethical or unethical, right or wrong, may not be the same somewhere else in the world. The first civilizations begun in Africa and Europe many thousands of years ago when people were hunters (...) and nomads, it is not unreasonable to suspect that many of those traits and characteristics have been socially transferred and/or inherited by future generations. (shrink)

Consider the view that coming into existence is bad for us. Can we hold this and yet deny that ceasing to exist would be good for us? I argue that we can. First, many animals have lives such that they would be better off not existing. Second, if persons and babies are distinct things then the same is true of babies. Third, even if persons and babies are not distinct things – rather they are phases that human beings go through (...) – still it is bad for babies that they come into existence. So it was bad for us to come into existence. But most of us now enjoy worthwhile lives. So it would be bad for us, now, to cease to exist. (shrink)

Many epistemological problems can be solved by the objective Bayesian view that there are rationality constraints on priors, that is, inductive probabilities. But attempts to work out these constraints have run into such serious problems that many have rejected objective Bayesianism altogether. I argue that the epistemologist should borrow the metaphysician’s concept of naturalness and assign higher priors to more natural hypotheses.

We used social network analysis to examine a theoretical model exploring why, and under what circumstances, the perpetrators’ ostracizing behaviors are accurately perceived by the target employees. In turn, these perceptions of ostracism lead to the target employees’ counterproductive work behaviors. Adopting perspectives from both perpetrators and targets, we directly measured the ostracizing behaviors by all potential perpetrators and perceived workplace ostracism by target employees. We integrate Social information processing theory and conservation of resource theory to propose a moderated mediation (...) model, and found that employees who have a high level of need to belong are more likely to capture coworkers’ ostracizing behaviors, and those with low political skill are more likely to engage in counterproductive work behavior as their reaction to perceived workplace ostracism. Theoretical and practical implications are discussed. (shrink)

Formal methods are changing how epistemology is being studied and understood. A Critical Introduction to Formal Epistemology introduces the types of formal theories being used and explains how they are shaping the subject. Beginning with the basics of probability and Bayesianism, it shows how representing degrees of belief using probabilities informs central debates in epistemology. As well as discussing induction, the paradox of confirmation and the main challenges to Bayesianism, this comprehensive overview covers objective chance, peer disagreement, the concept of (...) full belief, and the traditional problems of justification and knowledge. Subjecting each position to a critical analysis, it explains the main issues in formal epistemology, and the motivations and drawbacks of each position. Written in an accessible language and supported study questions, guides to further reading and a glossary, positions are placed in an historic context to give a sense of the development of the field. As the first introductory textbook on formal epistemology, A Critical Introduction to Formal Epistemology is an invaluable resource for students and scholars of contemporary epistemology. (shrink)

Sometimes we learn what the world is like, and sometimes we learn where in the world we are. Are there any interesting differences between the two kinds of cases? The main aim of this article is to argue that learning where we are in the world brings into view the same kind of observation selection effects that operate when sampling from a population. I will first explain what observation selection effects are ( Section 1 ) and how they are relevant (...) to learning where we are in the world ( Section 2 ). I will show how measurements in the Many Worlds Interpretation of quantum mechanics can be understood as learning where you are in the world via some observation selection effect ( Section 3 ). I will apply a similar argument to the Sleeping Beauty Problem ( Section 4 ) and explain what I take the significance of the analogy to be ( Section 5 ). Finally, I will defend the Restricted Principle of Indifference on which some of my arguments depend ( Section 6 ). (shrink)

Jurgen Habermas has argued that carrying out pre-natal germline enhancements would be inimical to the future child's autonomy. In this article, I suggest that many of the objections that have been made against Habermas' arguments by liberals in the enhancement debate misconstrue his claims. To explain why, I begin by explaining how Habermas' view of personal autonomy confers particular importance to the agent's embodiment and social environment. In view of this, I explain that it is possible to draw two arguments (...) against germline enhancements from Habermas' thought. I call these arguments ‘the argument from negative freedom’ and ‘the argument from natality’. Although I argue that many of the common liberal objections to Habermas are not applicable when his arguments are properly understood, I go on to suggest ways in which supporters of enhancement might appropriately respond to Habermas' arguments. (shrink)

Contemporary emphasis on creating culturally relevant and context specific knowledge increasingly drives researchers to conduct their work in settings outside their home country. This often requires researchers to build relationships with various stakeholders who may have a vested interest in the research. This case study examines the tension between relationship development with stakeholders and maintaining study integrity, in the context of potential harms, data credibility and cultural sensitivity. We describe an ethical breach in the conduct of global health research by (...) a arising from the ad-hoc participation of a community stakeholder external to the visiting research group. A framework for reflection is developed from a careful examination of underlying factors and presented with a discussion of consequences and mitigation measures. This framework aims to present lessons learned for researchers working abroad who might face similar situations in their work. (shrink)

Since the publication of Kenneth Howard’s 2017 article, “The Religion Singularity: A Demographic Crisis Destabilizing and Transforming Institutional Christianity,” there has been an increasing demand to understand the root causes and historical foundations for why institutional Christianity is in a state of de-institutionalization. In response to Howard’s research, a number of authors have sought to provide a contextual explanation for why the religion singularity is currently happening, including studies in epistemology, church history, psychology, anthropology, and church ministry. The purpose of (...) this article is to offer a brief survey and response to these interactions with Howard’s research, identifying the overall implications of each researcher’s perspective for understanding the religion singularity phenomenon. It explores factors relating to denominational switching in Jeshua Branch’s research, social memory in John Lingelbach’s essay, religious politics in Kevin Seybold’s survey, scientific reductionism in Jack David Eller’s position paper, and institutional moral failure in Brian McLaren’s article. (shrink)

Sober and Elgin defend the claim that there are a priori causal laws in biology. Lange and Rosenberg take issue with this on Humean grounds, among others. I will argue that Sober and Elgin don’t go far enough – there are a priori causal laws in many sciences. Furthermore, I will argue that this thesis is compatible with a Humean metaphysics and an empiricist epistemology.

Cian Dorr (2002) gives an argument for the 1/3 position in Sleeping Beauty. I argue this is based on a mistake about Sleeping Beauty's epistemic position.

Controlling Natality - the ratio of births to the general population - is one of the best means a state has to control its demographic composition. However, the fact that the state has certain interests with regard to the size and composition of its population does not necessarily give it the right to set and pursue natality policies, because such policies can potentially infringe on various human rights such as the rights of women and the rights of minorities. Using a (...) feminist perspective I first argue that even if it is illegitimate for states to try to influence people's choice as to the number of their children in order to achieve demographic change, the state may, and should, enact natality policies aimed at promoting women's right to equality, regardless of whether their end result is to achieve a demographic change. Next I examine whether states are allowed to pursue natality policies that are aimed at decreasing natality rates in specific cultural groups, whose cultural precepts are oppressive to women and dictate very high natality rates. Using the ultra orthodox Jewish community in Israel as a test case, I present and reject three objections to the state's right to pursue such natality policies: the objection from free choice, the objection from free association, and the objection from culture. Rejecting these objections I conclude that not only is the state allowed, but it is indeed obligated, to pursue natality policies that aim to alleviate the oppression of women by decreasing inordinately high birth rates in illiberal communities. However, when choosing the measures for the implementation of such policies the state must take care to choose only measures that respect human rights. (shrink)

The main argument given for relevant alternatives theories of knowledge has been that they answer scepticism about the external world. I will argue that relevant alternatives also solve two other problems that have been much discussed in recent years, a) the bootstrapping problem and b) the apparent conflict between semantic externalism and armchair self-knowledge. Furthermore, I will argue that scepticism and Mooreanism can be embedded within the relevant alternatives framework.

There are three main categories of rationale for withholding information or telling lies: if overwhelming harm can only be averted through deceit; complete triviality such that it is irrelevant whether the truth is told; a duty to protect the interests of others. Public health authorities are frequently having to form judgements about the public interest, whether to release information or issue warnings. In June 1992, routine surveillance detected patulin levels (a known carcinogen) in samples of apple juice exceeding safety threshold. (...) Remedial actions were promptly taken and it was planned to subsequently publish the information in the routine way. However, the media portrayed the handling of the problem as a conspiracy and there was a short term reduction in juice sales. In October 1995, the UK Committee on Safety of Medicines issued a warning about certain brands of the contraceptive pill, based on the interim results of three unpublished studies. The increased risk of thromboembolism was small, but the resulting scare led to an increase in unwanted pregnancies. The handling of the B.S.E. crisis in the U.K. also led to accusations of incompetence or conspiracy. Public health authorities have to handle uncertainty and frequently have to form judgements for public safety on the basis of evidence of poor quantity and quality. Their task is not helped by the sometimes conflicting agenda of scientists and media. The public also have differing perceptions and interpretations of risk. The series of scares and crises are having a detrimental effect on public confidence in public health authorities. (shrink)

The authors discussed the reasons for the recent economic collapse as caused by the lack of large businesses and global corporations losing touch with the people they serve. Losing touch has caused a distancing of understanding of the customers as people by these businesses and corporations. An antidote to this is that decisions that have to be made in global businesses as well as domestic organizations reflect some level of empathy. The objective is to highlight the fact that these businesses (...) are corporate citizens and in themselves must be aware of the culture in which they conduct themselves. The authors discuss how empathie decision-making can become part of the corporate fabric without losing any sense of appropriate business judgment. A process is defined to enable the empathie process. Finally, a straw man is set up to fund/enable the process while creating a positive and profitable business environment. (shrink)

During the perinatal period, the establishment of the attachment relationship with the fetus and subsequently with the real child is crucial for the parents' and the child's well-being. Coherently with the assumption that the attachment relationship starts to develop during pregnancy, this systematic review aims to analyze and systematize studies focused on the association between pre-natal attachment and parent-to-infant attachment, in order to clarify the emerging results and provide useful information for clinical purposes. Nineteen studies were included. Sixteen researches identified (...) a positive relationship between pre-natal attachment and parent-to-infant attachment, and three articles highlighted a negative association between antenatal attachment and post-partum bonding disorders. These results were found both in women and men, in normative and at-risk pregnancies, adopting different assessment approaches. However, only small or moderate associations were found. Future studies are needed to further confirm these findings across different populations and with different methodological approaches. Moreover, studies would be needed in order to clarify mechanisms through which pre-natal attachment influences parent-to-infant attachment, as well as protective and risk factors which intervene between these two variables. (shrink)

From an ontological foundation of natality, drawing from Hannah Arendt and Adriana Cavarero, this paper concludes that sexual violence uniquely undermines being-in-theworld and being-in-the-world-with-others. The framework of natality is not usually directly applied to sexual violence. Natality roots us ontologically in birth, beginnings and relationality. While the promise of the natal inclines the subject outwards, towards others, the horror of rape freezes victims in objectification, exploits exposure and entangles victims physically and psychically with their abuser. Sexual violence is the very (...) antitheses to the promise of the natal. (shrink)